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author | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-06-08 11:59:33 +0200 |
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committer | Justin Lecher (jlec) <jlec@j-schmitz.net> | 2009-06-08 11:59:33 +0200 |
commit | 2bdd97faa1c9f57f3d8d9d91fc6c439f260d809e (patch) | |
tree | fc363a9fddb9efa01920803d14fc6f43a495a14b /sci-chemistry/coot/files | |
parent | pymol live ebuild added (diff) | |
download | sci-2bdd97faa1c9f57f3d8d9d91fc6c439f260d809e.tar.gz sci-2bdd97faa1c9f57f3d8d9d91fc6c439f260d809e.tar.bz2 sci-2bdd97faa1c9f57f3d8d9d91fc6c439f260d809e.zip |
live coot added
Diffstat (limited to 'sci-chemistry/coot/files')
-rw-r--r-- | sci-chemistry/coot/files/9999-as-needed.patch | 485 |
1 files changed, 485 insertions, 0 deletions
diff --git a/sci-chemistry/coot/files/9999-as-needed.patch b/sci-chemistry/coot/files/9999-as-needed.patch new file mode 100644 index 000000000..6d45efac3 --- /dev/null +++ b/sci-chemistry/coot/files/9999-as-needed.patch @@ -0,0 +1,485 @@ +diff -ur analysis/Makefile.am analysis/Makefile.am +--- analysis/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ analysis/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -9,6 +9,7 @@ + $(MMDB_CXXFLAGS) + + libcoot_analysis_la_SOURCES = bfkurt.cc ++libcoot_analysis_la_LIBADD = $(top_builddir)/coot-utils/libcoot-coord-utils.la + + bin_PROGRAMS = bfactan + +@@ -16,7 +17,6 @@ + + bfactan_LDADD = \ + libcoot-analysis.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(CLIPPER_LIBS) \ +diff -ur coords/Makefile.am coords/Makefile.am +--- coords/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ coords/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -37,4 +37,6 @@ + libcoot_coords_la_SOURCES = Bond_lines.cc Cartesian.cc cos-sin.cc \ + mmdb-extras.cc utils.cc mmdb.cc mmdb-crystal.cc \ + Bond_lines_ext.cc coot-close.cc +- ++libcoot_coords_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/mini-mol/libcoot-mini-mol.la +diff -ur cootaneer/Makefile.am cootaneer/Makefile.am +--- cootaneer/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ cootaneer/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -34,6 +34,7 @@ + buccaneer-sequence.cpp cootaneer-sequence.cpp \ + buccaneer-lib.h buccaneer-prot.h \ + buccaneer-sequence.h cootaneer-sequence.h ++libcootaneer_la_LIBADD = $(CLIPPER_LIBS) + + subpkgdatadir = $(pkgdatadir) + subpkgdata_DATA = cootaneer-llk-2.40.dat +diff -ur coot-surface/Makefile.am coot-surface/Makefile.am +--- coot-surface/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ coot-surface/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -25,3 +25,4 @@ + + libcoot_surface_la_SOURCES = \ + coot-surface.cc coot-surface.hh rgbreps.cc rgbreps.h ++libcoot_surface_la_LIBADD = $(top_builddir)/surface/libccp4mg-surface.la +diff -ur coot-utils/Makefile.am coot-utils/Makefile.am +--- coot-utils/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ coot-utils/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -51,9 +51,11 @@ + # for pure coordinates (mmdb) things + libcoot_coord_utils_la_SOURCES = coot-coord-utils.cc \ + coot-coord-utils-nucleotides.cc coot-rama.cc ++libcoot_coord_utils_la_LIBADD = $(CLIPPER_LIBS) libcoot-utils.la + + # shelx + libcoot_shelx_la_SOURCES = coot-shelx-ins.cc ++libcoot_shelx_la_LIBADD = $(MMDB_LIBS) libcoot-coord-utils.la + + # for non-simple coordinates things + libcoot_coord_extras_la_SOURCES = coot-coord-extras.cc coot-coord-lsq.cc +@@ -63,21 +65,20 @@ + + # for map things that need mmdb, clipper, gsl and other things + libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc ++libcoot_map_heavy_la_LIBADD = $(GSL_LIBS) + + noinst_PROGRAMS = testshelxreader testcootutils + + testshelxreader_SOURCES = test-shelx-reader.cc + testshelxreader_LDADD = \ + ./libcoot-shelx.la \ +- ./libcoot-coord-utils.la \ +- ./libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ ./libcoot-utils.la + + testcootutils_SOURCES = test-utils.cc + testcootutils_LDADD = \ + ./libcoot-shelx.la \ + ./libcoot-coord-utils.la \ + ./libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(MMDB_LIBS) + + +--- geometry/Makefile.am 2008-09-08 15:22:01.000000000 +0200 ++++ geometry/Makefile.am.new 2008-11-20 12:01:08.000000000 +0100 +@@ -35,6 +35,10 @@ + + libcoot_geometry_la_SOURCES = protein-geometry.cc protein-geometry-mmdb.cc + ++libcoot_geometry_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-utils.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) ++ + # libcoot_geometry_la_CXXFLAGS = -g -O1 + + noinst_PROGRAMS = test-geometry test-read-components +@@ -43,12 +47,6 @@ + + test_read_components_SOURCES = test-read-components.cc test-read-components.hh + +-test_geometry_LDADD = ./libcoot-geometry.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) +- +-test_read_components_LDADD = \ +- ./libcoot-geometry.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++test_geometry_LDADD = ./libcoot-geometry.la + ++test_read_components_LDADD = ./libcoot-geometry.la + +diff -ur ideal/Makefile.am ideal/Makefile.am +--- ideal/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ ideal/Makefile.am 2008-07-13 16:41:14.000000000 -0700 +@@ -44,6 +44,12 @@ + AM_CXXFLAGS = $(COOT_GSL_FLAGS) $(GSL_CFLAGS) + + libcoot_ideal_la_SOURCES = simple-restraint.cc pepflip.cc regularize-minimol.cc lograma.cpp ++libcoot_ideal_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-utils.la \ ++ $(top_builddir)/mini-mol/libcoot-mini-mol.la \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ ++ $(GSL_LIBS) + + noinst_PROGRAMS = test-indexing with-geometry with-map logramatest + # bin_PROGRAMS = +@@ -63,36 +69,25 @@ + with_geometry_LDADD = \ + ./libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + # add libcoot-map-utils for the debugging density_around_point function + with_map_LDADD = \ + ./libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/compat/libcoot-compat.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ ++ $(top_builddir)/compat/libcoot-compat.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + test_indexing_LDADD = \ + ./libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) ++ $(CLIPPER_LIBS) $(MMDB_LIBS) + + # Why do I need all these libraries to simply link a trivial test program? + # Badness.... +diff -ur mini-mol/Makefile.am mini-mol/Makefile.am +--- mini-mol/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ mini-mol/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -32,8 +32,9 @@ + testminimol_SOURCES = testminimol.cc + + libcoot_mini_mol_la_SOURCES = mini-mol.cc mini-mol-utils.cc ++libcoot_mini_mol_la_LIBADD = \ ++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ ++ $(CLIPPER_LIBS) + + testminimol_LDADD = libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(CLIPPER_LIBS) $(MMDB_LIBS) ++ $(MMDB_LIBS) +diff -ur skeleton/Makefile.am skeleton/Makefile.am +--- skeleton/Makefile.am 2008-07-13 16:40:27.000000000 -0700 ++++ skeleton/Makefile.am 2008-07-13 16:40:40.000000000 -0700 +@@ -36,7 +36,7 @@ + + + libcoot_skeleton_la_SOURCES = $(libskeleton_a_sources) +- ++libcoot_skeleton_la_LIBADD = ../atom-utils/libcoot-atomutils.la + + # bin_PROGRAMS = ncssearch test_various test_torsion test_theta_2 + +--- high-res/Makefile.am 2009-01-06 20:19:20.000000000 +0100 ++++ high-res/Makefile.am.new 2009-06-03 10:13:35.000000000 +0200 +@@ -39,13 +39,17 @@ + + libcoot_high_res_la_SOURCES = high-res.cc coot-atom-graph.cc residue-distortions.cc \ + sequence-assignment.cc ++libcoot_high_res_la_LIBADD = \ ++ $(top_builddir)/ligand/libcoot-ligand.la \ ++ $(top_builddir)/coot-utils/libcoot-map-utils.la \ ++ $(CLIPPER_LIBS) $(MMDB_LIBS) ++ + + check_PROGRAMS = testatomgraph tracehighres testseqalign testseqassignment globularize_protein + + testatomgraph_SOURCES = test-atom-graph.cc + + testatomgraph_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ +@@ -53,71 +57,60 @@ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + testseqassignment_SOURCES = testseqassignment.cc + testseqassignment_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + # tracehighres_LDFLAGS = -static + tracehighres_SOURCES = trace-high-res.cc + tracehighres_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + + testseqalign_SOURCES = testseqalign.cc + + # why do we need to link with all this (junk)? + testseqalign_LDADD = libcoot-high-res.la \ +- $(top_builddir)/ligand/libcoot-ligand.la \ + $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ + $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ + $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ +- $(GSL_LIBS) \ +- $(CLIPPER_LIBS) ++ $(GSL_LIBS) + + + globularize_protein_SOURCES = globularize.cc +--- ligand/Makefile.am 2009-02-06 00:50:01.000000000 +0100 ++++ ligand/Makefile.am.new 2009-06-03 10:29:30.000000000 +0200 +@@ -50,6 +50,18 @@ + torsion-general.cc rotamer-tables.cc primitive-chi-angles.cc dipole.cc\ + base-pairing.cc + ++libcoot_ligand_la_LIBADD = \ ++ $(top_builddir)/ideal/libcoot-ideal.la \ ++ $(top_builddir)/coords/libcoot-coords.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-extras.la \ ++ $(top_builddir)/coot-utils/libcoot-map-utils.la \ ++ $(top_builddir)/db-main/libcoot-db-main.la \ ++ $(top_builddir)/coot-utils/libcoot-shelx.la \ ++ $(top_builddir)/geometry/libcoot-geometry.la \ ++ $(top_builddir)/coot-utils/libcoot-coord-utils.la \ ++ $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la ++ ++ + AM_CXXFLAGS = \ + -DPKGDATADIR='"$(pkgdatadir)"' \ + $(COOT_WINDOWS_CFLAGS) +@@ -69,52 +81,25 @@ + + test_random_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + test_ligand_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + test_helix_placement_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + +@@ -122,19 +107,10 @@ + + test_fffear_in_coot_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ + $(top_builddir)/coot-utils/libcoot-map-heavy.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + +@@ -146,23 +122,13 @@ + + findligand_real_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(top_builddir)/compat/libcoot-compat.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + findwaters_real_LDADD = \ + ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/geometry/libcoot-geometry.la \ + $(top_builddir)/coords/libcoot-coords.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +@@ -193,17 +159,8 @@ + testdunbrack_SOURCES = testdunbrack.cc + + testdunbrack_LDADD = ./libcoot-ligand.la \ +- $(top_builddir)/ideal/libcoot-ideal.la \ + $(top_builddir)/mini-mol/libcoot-mini-mol.la \ +- $(top_builddir)/geometry/libcoot-geometry.la \ +- $(top_builddir)/coords/libcoot-coords.la \ +- $(top_builddir)/ccp4mg-utils/libccp4mg-utils.la \ +- $(top_builddir)/coot-utils/libcoot-map-utils.la \ +- $(top_builddir)/db-main/libcoot-db-main.la \ +- $(top_builddir)/coot-utils/libcoot-coord-extras.la \ +- $(top_builddir)/coot-utils/libcoot-coord-utils.la \ + $(top_builddir)/coot-utils/libcoot-utils.la \ +- $(top_builddir)/coot-utils/libcoot-shelx.la \ + $(CLIPPER_LIBS) $(MMDB_LIBS) $(GSL_LIBS) + + # lib coot-coords depends on mmdb, even though Cartesian doesn't +--- tw/Makefile.am 2007-04-20 16:12:16.000000000 +0200 ++++ tw/Makefile.am.new 2009-06-03 10:31:17.000000000 +0200 +@@ -39,14 +39,16 @@ + include_HEADERS = coot-tw.hh + + libcoot_tw_la_SOURCES = tw.cc ++libcoot_tw_la_LIBADD = \ ++ $(GTKCANVAS_LIBS) \ ++ @GTK_LIBS@ ++ + + noinst_PROGRAMS = coot-tiddly + + coot_tiddly_SOURCES = tiddly.cc + +-coot_tiddly_LDADD = libcoot-tw.la \ +- $(GTKCANVAS_LIBS) \ +- @GTK_LIBS@ ++coot_tiddly_LDADD = libcoot-tw.la + + + # cootsound_LDADD = -L/sw/lib -lvorbisfile -logg -lao +--- Makefile.am 2009-01-06 15:50:23.000000000 +0100 ++++ Makefile.am.new 2009-06-03 10:35:59.000000000 +0200 +@@ -25,10 +25,10 @@ + + # see configure.in for po intl + SUBDIRS = auxil scheme python macros compat coot-utils surface coot-surface \ +- skeleton ccp4mg-utils density-contour coords angles \ +- mini-mol db-main geometry \ ++ atom-utils skeleton ccp4mg-utils density-contour mini-mol coords angles \ ++ db-main geometry \ + ideal ligand high-res build greg-tests python-tests \ +- analysis sequence-view tw atom-utils cootaneer src rama-data doc ++ analysis sequence-view tw cootaneer src rama-data doc + + # po, no po today. + +--- coot-utils/Makefile.am.orig 2009-06-07 17:40:00.000000000 -0700 ++++ coot-utils/Makefile.am 2009-06-07 17:39:07.000000000 -0700 +@@ -63,6 +63,7 @@ + + # for (map) things that need to link mmdb and clipper: + libcoot_map_utils_la_SOURCES = coot-map-utils.cc peak-search.cc trim.cc xmap-stats.cc ++libcoot_map_utils_la_LIBADD = $(CLIPPER_LIBS) + + # for map things that need mmdb, clipper, gsl and other things + libcoot_map_heavy_la_SOURCES = coot-map-heavy.cc coot-fffear.cc |